Proof-of-concept: SCENTinel 1.1 rapidly discriminates COVID-19-related olfactory disorders.

It is estimated that 20%-67% of those with COVID-19 develop olfactory disorders, depending on the SARS-CoV-2 variant. However, there is an absence of quick, population-wide olfactory tests to screen for olfactory disorders. The purpose of this study was to provide a proof-of-concept that SCENTinel 1.1, a rapid, inexpensive, population-wide olfactory test, can discriminate between anosmia (total smell loss), hyposmia (reduced sense of smell), parosmia (distorted odor perception), and phantosmia (odor sensation without a source). Participants were mailed a SCENTinel 1.1 test, which measures odor detection, intensity, identification, and pleasantness, using one of 4 possible odors. Those who completed the test (N = 287) were divided into groups based on their self-reported olfactory function: quantitative olfactory disorder only (anosmia or hyposmia, N = 135), qualitative olfactory disorder only (parosmia and/or phantosmia; N = 86), and normosmia (normal sense of smell; N = 66). SCENTinel 1.1 accurately discriminates quantitative olfactory disorders, qualitative olfactory disorders, and normosmia groups. When olfactory disorders were assessed individually, SCENTinel 1.1 discriminates between hyposmia, parosmia, and anosmia. Participants with parosmia rated common odors less pleasant than those without parosmia. We provide proof-of-concept that SCENTinel 1.1, a rapid smell test, can discriminate quantitative and qualitative olfactory disorders, and is the only direct test to rapidly discriminate parosmia.

Combined data analysis of fossil and living mammals: a Paleogene sister taxon of Placentalia and the antiquity of Marsupialia.

The Cretaceous-Paleogene (KPg) boundary, one of Earth's five major extinction events, occurred just before the appearance of Placentalia in the fossil record. The Gobi Desert, Mongolia and the Western Interior of North America have important fossil mammals occurring just before and after the KPg boundary (e.g. Prodiacodon, Deltatheridium) that have yet to be phylogenetically tested in a character-rich context with molecular data. We present here phylogenetic analyses of >6000 newly scored anatomical observations drawn from six untested fossils and added to the largest existing morphological matrix for mammals. These data are combined with sequence data from 27 nuclear genes. Results show the existence of a new eutherian sister clade to Placentalia, which we name and characterize. The extinct clade Leptictidae is part of this placental sister clade, indicating that the sister clade survived the KPg event to co-exist in ancient ecosystems during the Paleogene radiation of placentals. Analysing the Cretaceous metatherian Deltatheridium in this character-rich context reveals it is a member of Marsupialia, a finding that extends the minimum age of Marsupialia before the KPg boundary. Numerous shared-derived features from multiple anatomical systems support the assignment of Deltatheridium to Marsupialia. Computed tomography scans of exquisite new specimens better document the marsupial-like dental replacement pattern of Deltatheridium. The new placental sister clade has both Asian and North American species, and is ancestrally characterized by shared derived features such as a hind limb modified for saltatorial locomotion.

A dense sample of fossil primates (Adapiformes, Notharctidae, Notharctinae) from the Early Eocene Willwood Formation, Wyoming: Documentation of gradual change in tooth area and shape through time.

OBJECTIVES: The Willwood Formation of the southern Bighorn Basin, Wyoming is a fluvial rock sequence that spans approximately 3 million years of early Eocene time. It has yielded one the largest collections of fossil mammals in the world including thousands of dentitions of extinct lemur-like primates known as notharctines. In the southern Bighorn Basin, specimens of these primates have been collected on numerous paleontological expeditions and the stratigraphic levels yielding the dentitions have been carefully recorded. Notharctine dentitions represent a rare opportunity to study morphological variation in a single anatomical system through time among closely related individuals. MATERIALS AND METHODS: Prior studies of Bighorn Basin notharctines through time produced measurements of hundreds of specimens but I report here results from measurement and comparison of the dentitions and dentaries of more than 3,000 specimens, all stratigraphically mapped. RESULTS: Variation in premolar and molar area and variation in dentary depth are apparent throughout the section. Specimens with relatively small teeth and dentaries are known from the older part of the section. In younger rocks, variation in tooth area among specimens increases. Variation in tooth area is continuous and overlaps extensively both within and between stratigraphic levels. Other dental variables examined by inspection change in a mosaic and continuous fashion through the section. These features include variation in the presence and number of paraconids on the lower fourth premolar (p4), the size and shape of the entoconid notch on the lower first and second molars, and the relative development of the pseudohypocone, mesostyle, and cingula on the upper molars. DISCUSSION: These broad patterns can be identified despite notharctine alpha taxonomy being in need of extensive revision and, importantly, simplification. Such revision is beyond the scope of this article but is essential if we are to develop a taxonomy that is both free of stratigraphic influence and useful for rapid, repeatable species assignment. Boundaries among the patterns of tokogenesis, anagenesis, and cladogenesis are blurred in this dense sample of extinct primates. While pattern of evolution, a population-level phenomenon, may be difficult to falsify in the fossil record, this notharctine sample suggests that in the rare instance such as this, when the fossil record is densely sampled, change through time is continuous and more consistent with gradual evolution.

Crowds Replicate Performance of Scientific Experts Scoring Phylogenetic Matrices of Phenotypes.

Scientists building the Tree of Life face an overwhelming challenge to categorize phenotypes (e.g., anatomy, physiology) from millions of living and fossil species. This biodiversity challenge far outstrips the capacities of trained scientific experts. Here we explore whether crowdsourcing can be used to collect matrix data on a large scale with the participation of nonexpert students, or "citizen scientists." Crowdsourcing, or data collection by nonexperts, frequently via the internet, has enabled scientists to tackle some large-scale data collection challenges too massive for individuals or scientific teams alone. The quality of work by nonexpert crowds is, however, often questioned and little data have been collected on how such crowds perform on complex tasks such as phylogenetic character coding. We studied a crowd of over 600 nonexperts and found that they could use images to identify anatomical similarity (hypotheses of homology) with an average accuracy of 82% compared with scores provided by experts in the field. This performance pattern held across the Tree of Life, from protists to vertebrates. We introduce a procedure that predicts the difficulty of each character and that can be used to assign harder characters to experts and easier characters to a nonexpert crowd for scoring. We test this procedure in a controlled experiment comparing crowd scores to those of experts and show that crowds can produce matrices with over 90% of cells scored correctly while reducing the number of cells to be scored by experts by 50%. Preparation time, including image collection and processing, for a crowdsourcing experiment is significant, and does not currently save time of scientific experts overall. However, if innovations in automation or robotics can reduce such effort, then large-scale implementation of our method could greatly increase the collective scientific knowledge of species phenotypes for phylogenetic tree building. For the field of crowdsourcing, we provide a rare study with ground truth, or an experimental control that many studies lack, and contribute new methods on how to coordinate the work of experts and nonexperts. We show that there are important instances in which crowd consensus is not a good proxy for correctness.

Giant taxon-character matrices: the future of morphological systematics.

Simões et al. () argued that large matrices are linked to the construction of "problematic" characters, and that those characters negatively affect tree topology. In their re-evaluation of two squamate datasets, however, Simões et al. () simply eliminated what they termed "problematic" characters, rather than recode them. This practice ignores potential sources of phylogenetic information and, if it were to be more widely followed, would inhibit the advancement of the field of systematics. Here, we defend the necessity and inevitability of large morphological (phenomic) datasets and discuss best practices for morphological data collection in contemporary phylogenetics.

Phylogeny of the North American catfish family Ictaluridae (Teleostei: Siluriformes) combining morphology, genes and fossils.

We performed the first combined-data phylogenetic analysis of ictalurids including most living and fossil species. We sampled 56 extant species and 16 fossil species representing outgroups, the seven living genera, and the extinct genus †Astephus long thought to be an ictalurid. In total, 209 morphological characters were curated and illustrated in MorphoBank from published and original work, and standardized using reductive coding. Molecular sequences harvested from GenBank for one nuclear and four mitochondrial genes were combined with the morphological data for total evidence analysis. Parsimony analysis recovers a crown clade Ictaluridae composed of seven living genera and numerous extinct species. The oldest ictalurid fossils are the Late Eocene members of Ameiurus and Ictalurus. The fossil clade †Astephus placed outside of Ictaluridae and not as its sister taxon. Previous morphological phylogenetic studies of Ictaluridae hypothesized convergent evolution of troglobitic features among the subterranean species. In contrast, we found morphological evidence to support a single clade of the four troglobitic species, the sister taxon of all ictalurids. This result holds whether fossils are included or not. Some previously published clock-based age estimates closely approximate our minimum ages of clades.

Proof-of-concept: SCENTinel 1.1 rapidly discriminates COVID-19 related olfactory disorders.

It is estimated that 20-67% of those with COVID-19 develop olfactory disorders, depending on the SARS-CoV-2 variant. However, there is an absence of quick, population-wide olfactory tests to screen for olfactory disorders. The purpose of this study was to provide a proof-of-concept that SCENTinel 1.1, a rapid, inexpensive, population-wide olfactory test, can discriminate between anosmia (total smell loss), hyposmia (reduced sense of smell), parosmia (distorted odor perception), and phantosmia (odor sensation without a source). Participants were mailed a SCENTinel 1.1 test, which measures odor detection, intensity, identification, and pleasantness, using one of four possible odors. Those who completed the test (N = 381) were divided into groups based on their self-reported olfactory function: quantitative olfactory disorder (anosmia or hyposmia, N = 135), qualitative olfactory disorder (parosmia and/or phantosmia; N = 86), and normosmia (normal sense of smell; N = 66). SCENTinel 1.1 accurately discriminates quantitative olfactory disorders, qualitative olfactory disorders, and normosmia groups. When olfactory disorders were assessed individually, SCENTinel 1.1 discriminates between hyposmia, parosmia and anosmia. Participants with parosmia rated common odors less pleasant than those without parosmia. We provide proof-of-concept that SCENTinel 1.1, a rapid smell test, can discriminate quantitative and qualitative olfactory disorders, and is the only direct test to rapidly discriminate parosmia.

MorphoBank: phylophenomics in the "cloud".

A highly interoperable informatics infrastructure rapidly emerged to handle genomic data used for phylogenetics and was instrumental in the growth of molecular systematics. Parallel growth in software and databases to address needs peculiar to phylophenomics has been relatively slow and fragmented. Systematists currently face the challenge that Earth may hold tens of millions of species (living and fossil) to be described and classified. Grappling with research on this scale has increasingly resulted in work by teams, many constructing large phenomic supermatrices. Until now, phylogeneticists have managed data in single-user, file-based desktop software wholly unsuitable for real-time, team-based collaborative work. Furthermore, phenomic data often differ from genomic data in readily lending themselves to media representation (e.g. 2D and 3D images, video, sound). Phenomic data are a growing component of phylogenetics, and thus teams require the ability to record homology hypotheses using media and to share and archive these data. Here we describe MorphoBank, a web application and database leveraging software as a service methodology compatible with "cloud" computing technology for the construction of matrices of phenomic data. In its tenth year, and fully available to the scientific community at-large since inception, MorphoBank enables interactive collaboration not possible with desktop software, permitting self-assembling teams to develop matrices, in real time, with linked media in a secure web environment. MorphoBank also provides any user with tools to build character and media ontologies (rule sets) within matrices, and to display these as directed acyclic graphs. These rule sets record the phylogenetic interrelatedness of characters (e.g. if X is absent, Y is inapplicable, or X-Z characters share a media view). MorphoBank has enabled an order of magnitude increase in phylophenomic data collection: a recent collaboration by more than 25 researchers has produced a database of > 4500 phenomic characters supported by > 10 000 media. © The Willi Hennig Society 2011.

Impact of increased character sampling on the phylogeny of Cetartiodactyla (Mammalia): combined analysis including fossils.

The phylogenetic position of Cetacea (whales, dolphins and porpoises) is an important exemplar problem for combined data parsimony analyses because the clade is ancient and includes many well-known and relatively complete fossil species. We combined data for 71 terminal taxa (43 extinct/28 extant) to test where Cetacea fits within Cetartiodactyla, and where various fossil hoofed mammals (e.g., †entelodonts, "†anthracotheriids" and †mesonychians) are positioned. We scored 635 phenotypic characters (osteology, dentition, soft tissue, behavior), approximately three times the number of characters in the last major analysis of this clade, and combined these with > 40 000 molecular characters, including new data from 10 genes. The analysis supported a topology consistent with the majority of recently published molecular studies. Cetacea was the extant sister taxon of Hippopotamidae, followed successively by Ruminantia, Suina and Camelidae. Several extinct taxa were phylogenetically unstable, upsetting resolution of the strict consensus and limiting branch support, but the positions of several key fossils were consistently resolved. The wholly extinct †Mesonychia was more closely related to Cetacea than was any "artiodactylan.""†Anthracotheriids" were paraphyletic, and, with the exception of one species, were more closely related to Hippopotamidae than to any other living taxon. The total evidence analysis overturned a highly nested position for Moschus supported by molecular data alone. The character partition that could be scored for the fossil taxa (osteological and dental characters) included more informative characters than most molecular partitions in our analysis, and had the fewest missing data. The osteological-dental data alone, however, did not support inclusion of cetaceans within crown "Artiodactyla." Recently discovered ankle bones from fossil whales reinforced the monophyly of Cetartiodactyla but provided no particular evidence of derived similarities between hippopotamids and fossil cetaceans that were not shared with other "artiodactylans". © The Willi Hennig Society 2007.

The Origin of Large-Bodied Shrimp that Dominate Modern Global Aquaculture.

Several shrimp species from the clade Penaeidae are farmed industrially for human consumption, and this farming has turned shrimp into the largest seafood commodity in the world. The species that are in demand for farming are an anomaly within their clade because they grow to much larger sizes than other members of Penaeidae. Here we trace the evolutionary history of the anomalous farmed shrimp using combined data phylogenetic analysis of living and fossil species. We show that exquisitely preserved fossils of †Antrimpos speciosus from the Late Jurassic Solnhofen limestone belong to the same clade as the species that dominate modern farming, dating the origin of this clade to at least 145 mya. This finding contradicts a much younger Late Cretaceous age (ca. 95 mya) previously estimated for this clade using molecular clocks. The species in the farmed shrimp clade defy a widespread tendency, by reaching relatively large body sizes despite their warm water lifestyles. Small body sizes have been shown to be physiologically favored in warm aquatic environments because satisfying oxygen demands is difficult for large organisms breathing in warm water. Our analysis shows that large-bodied, farmed shrimp have more gills than their smaller-bodied shallow-water relatives, suggesting that extra gills may have been key to the clade's ability to meet oxygen demands at a large size. Our combined data phylogenetic tree also suggests that, during penaeid evolution, the adoption of mangrove forests as habitats for young shrimp occurred multiple times independently.

Sperm head morphology in 36 species of artiodactylans, perissodactylans, and cetaceans (Mammalia).

Detailed descriptions of mammalian sperm morphology across a range of closely related taxa are rare. Most contributions have been generalized descriptions of a few distantly related mammalian species. These studies have emphasized a generalized ungulate sperm morphology, but have not underscored several important morphological differences in ungulate sperm, such as head shape. The present study is the first to document descriptions of sperm head morphology using cold field-emission scanning electron microscopy (FE-SEM) for a large number of closely related mammalian species. In total, the sperm of 36 species in three orders: Artiodactyla (even-toed ungulates), Cetacea (whales, porpoises, and dolphins), and Perissodactyla (odd-toed ungulates) were examined to gather new information relevant to the debate about the phylogenetic placement of cetaceans relative to terrestrial ungulates. In all species examined, the sperm heads were generally flattened and ovate in shape with a distinct apical ridge, although considerable variation in sperm head shape was detected, both within and between orders. In artiodactylans, the sperm head was uniformly flat in lateral view, whereas perissodactylan and cetacean sperm heads showed a distinct posterior thickening. In both artiodactylans and perissodactylans, the mitochondria were elongate and wound in a tight helix around the midpiece, whereas in cetaceans the mitochondria were rounded and appeared to be randomly arranged around the midpiece. Additionally, prominent ridges running along the anterior-posterior axis were observed in the postacrosomal region of the sperm head in four species of cetaceans. These ridges were not observed in any of the terrestrial ungulates examined. Pits or fenestrations were detected in the postacrosomal region in most artiodactylan species examined; these structures were not detected in perissodactylans or cetaceans. The equatorial segment of the acrosome was detected in the artiodactylan species examined, tentatively identified in perissodactylans, but not found in cetaceans. Its shape and location are described for relevant taxa. The presence of a recently reported substructure within the equatorial segment (the equatorial subsegment; Ellis et al. [2002] J Struct Biol 138:187-198) was detected in artiodactylans, and its shape is described for the species examined.

A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway.

The CIPRES Science Gateway is a community web application that provides public access to a set of parallel tree inference and multiple sequence alignment codes run on large computational resources. These resources are made available at no charge to users by the NSF Extreme Science and Engineering Discovery Environment (XSEDE) project. Here we describe the CIPRES RESTful application programmer interface (CRA), a web service that provides programmatic access to all resources and services currently offered by the CIPRES Science Gateway. Software developers can use the CRA to extend their web or desktop applications to include the ability to run MrBayes, BEAST, RAxML, MAFFT, and other computationally intensive algorithms on XSEDE. The CRA also makes it possible for individuals with modest scripting skills to access the same tools from the command line using curl, or through any scripting language. This report describes the CRA and its use in three web applications (Influenza Research Database - www.fludb.org, Virus Pathogen Resource - www.viprbrc.org, and MorphoBank - www.morphobank.org). The CRA is freely accessible to registered users at https://cipresrest.sdsc.edu/cipresrest/v1; supporting documentation and registration tools are available at https://www.phylo.org/restusers.

Parsimony Analysis of Total Evidence from Extinct and Extant Taxa and the Cetacean-Artiodactyl Question (Mammalia, Ungulata).

Many molecule-based phylogenetic analyses find that the mammalian order Artiodactyla (even-toed ungulates) is paraphyletic unless cetaceans (whales, dolphins, and porpoises) are nested within it, a hypothesis that runs contrary to traditional morphology-based ideas. Here I present a total evidence analysis of this question based on 10 extant and 27 extinct taxa, using two character data partitions: (i) skeletal data and (ii) neontological data (soft morphology, retroposons, and DNA sequences [γ-fibrinogen, ß-casein, and κ-casein and mt cytochrome b]). A sensitivity analysis varying gap cost and transversion/transition ratio over nine parameters was implemented in the sequence alignment and in the parsimony analysis. The two data partitions are significantly incongruent, and the neontological data partition includes over six times as many characters as the osteological data partition. The osteological data partition, however, samples almost three times more taxa, taxa that cannot be sampled for neontological data because they are extinct. Osteological data resulted in artiodactyl monophyly, and neontological data resulted in artiodactyl paraphyly over all nine parameters. In the total evidence analysis the parameter most congruent with the overall character data is unresolved as to the sister taxon of Cetacea; however, the Adams consensus tree favors the neontological result. Extinction of almost 90% of the clade and particularly poor knowledge of stem taxa at the base of Artiodactyla make resolution of conflicting molecule- and morphology-based phylogenetic signals particularly difficult.

Best practices for data sharing in phylogenetic research.

As phylogenetic data becomes increasingly available, along with associated data on species' genomes, traits, and geographic distributions, the need to ensure data availability and reuse become more and more acute. In this paper, we provide ten "simple rules" that we view as best practices for data sharing in phylogenetic research. These rules will help lead towards a future phylogenetics where data can easily be archived, shared, reused, and repurposed across a wide variety of projects.

Response to comment on "The placental mammal ancestor and the post-K-Pg radiation of placentals".

Tree-building with diverse data maximizes explanatory power. Application of molecular clock models to ancient speciation events risks a bias against detection of fast radiations subsequent to the Cretaceous-Paleogene (K-Pg) event. Contrary to Springer et al., post-K-Pg placental diversification does not require "virus-like" substitution rates. Even constraining clade ages to their model, the explosive model best explains placental evolution.

The placental mammal ancestor and the post-K-Pg radiation of placentals.

To discover interordinal relationships of living and fossil placental mammals and the time of origin of placentals relative to the Cretaceous-Paleogene (K-Pg) boundary, we scored 4541 phenomic characters de novo for 86 fossil and living species. Combining these data with molecular sequences, we obtained a phylogenetic tree that, when calibrated with fossils, shows that crown clade Placentalia and placental orders originated after the K-Pg boundary. Many nodes discovered using molecular data are upheld, but phenomic signals overturn molecular signals to show Sundatheria (Dermoptera + Scandentia) as the sister taxon of Primates, a close link between Proboscidea (elephants) and Sirenia (sea cows), and the monophyly of echolocating Chiroptera (bats). Our tree suggests that Placentalia first split into Xenarthra and Epitheria; extinct New World species are the oldest members of Afrotheria.

Next-generation phenomics for the Tree of Life.

The phenotype represents a critical interface between the genome and the environment in which organisms live and evolve. Phenotypic characters also are a rich source of biodiversity data for tree building, and they enable scientists to reconstruct the evolutionary history of organisms, including most fossil taxa, for which genetic data are unavailable. Therefore, phenotypic data are necessary for building a comprehensive Tree of Life. In contrast to recent advances in molecular sequencing, which has become faster and cheaper through recent technological advances, phenotypic data collection remains often prohibitively slow and expensive. The next-generation phenomics project is a collaborative, multidisciplinary effort to leverage advances in image analysis, crowdsourcing, and natural language processing to develop and implement novel approaches for discovering and scoring the phenome, the collection of phentotypic characters for a species. This research represents a new approach to data collection that has the potential to transform phylogenetics research and to enable rapid advances in constructing the Tree of Life. Our goal is to assemble large phenomic datasets built using new methods and to provide the public and scientific community with tools for phenomic data assembly that will enable rapid and automated study of phenotypes across the Tree of Life.

Relationships of Cetacea (Artiodactyla) among mammals: increased taxon sampling alters interpretations of key fossils and character evolution.

BACKGROUND: Integration of diverse data (molecules, fossils) provides the most robust test of the phylogeny of cetaceans. Positioning key fossils is critical for reconstructing the character change from life on land to life in the water. METHODOLOGY/PRINCIPAL FINDINGS: We reexamine relationships of critical extinct taxa that impact our understanding of the origin of Cetacea. We do this in the context of the largest total evidence analysis of morphological and molecular information for Artiodactyla (661 phenotypic characters and 46,587 molecular characters, coded for 33 extant and 48 extinct taxa). We score morphological data for Carnivoramorpha, Creodonta, Lipotyphla, and the raoellid artiodactylan Indohyus and concentrate on determining which fossils are positioned along stem lineages to major artiodactylan crown clades. Shortest trees place Cetacea within Artiodactyla and close to Indohyus, with Mesonychia outside of Artiodactyla. The relationships of Mesonychia and Indohyus are highly unstable, however--in trees only two steps longer than minimum length, Mesonychia falls inside Artiodactyla and displaces Indohyus from a position close to Cetacea. Trees based only on data that fossilize continue to show the classic arrangement of relationships within Artiodactyla with Cetacea grouping outside the clade, a signal incongruent with the molecular data that dominate the total evidence result. CONCLUSIONS/SIGNIFICANCE: Integration of new fossil material of Indohyus impacts placement of another extinct clade Mesonychia, pushing it much farther down the tree. The phylogenetic position of Indohyus suggests that the cetacean stem lineage included herbivorous and carnivorous aquatic species. We also conclude that extinct members of Cetancodonta (whales+hippopotamids) shared a derived ability to hear underwater sounds, even though several cetancodontans lack a pachyostotic auditory bulla. We revise the taxonomy of living and extinct artiodactylans and propose explicit node and stem-based definitions for the ingroup.